Dear Galaxy Community,

I am a Ph.D. student working on Plasmodium Genome. My project mainly focuses on short  Amplicon sequence using Miseq platform and I have a total of 200 primers designed for targeted 200 loci on 14 chromosomes.  I would like to ask you which pipeline would be better to do demultiplex 200 primers/ sample for 96 samples (output from MiSeq),  quality filter, mapping reads and variant calling simultaneously. Since the majority of current pipelines (GATK and others) are designed for large reads and diploid organism like human. Any suggestion or comment highly appreciated for my data (short millions of multiplexed reads for a haploid organism)...

With Regards,

Abe